unmarkedFrameDSO: Create an object of class unmarkedFrameDSO that contains data...

In unmarked: Models for Data from Unmarked Animals

Create an object of class unmarkedFrameDSO that contains data used by distsampOpen.

Description

Organizes distance sampling data and experimental design information from multiple primary periods along with associated covariates. This S4 class is required by the data argument of distsampOpen

Usage

unmarkedFrameDSO(y, siteCovs=NULL, yearlySiteCovs=NULL, numPrimary, 
       primaryPeriod, dist.breaks, tlength, survey, unitsIn)

Arguments

y	An MxJT matrix of the repeated count data, where M is the number of sites (i.e., points or transects), J is the number of distance classes and T is the maximum number of primary sampling periods per site
siteCovs	A data.frame of covariates that vary at the site level. This should have M rows and one column per covariate
yearlySiteCovs	Either a named list of MxT data.frames, or a site-major data.frame with MT rows and 1 column per covariate
numPrimary	Maximum number of observed primary periods for each site
primaryPeriod	An MxJT matrix of integers indicating the primary period of each observation
dist.breaks	vector of distance cut-points delimiting the distance classes. It must be of length J+1
tlength	A vector of length R containing the transect lengths. This is ignored when survey="point"
survey	Either "point" or "line" for point- and line-transects
unitsIn	Either "m" or "km" defining the measurement units for both dist.breaks and tlength

Details

unmarkedFrameDSO is the S4 class that holds data to be passed to the distsampOpen model-fitting function. Unlike most unmarked functions, obsCovs cannot be supplied.

If you have continuous distance data, they must be "binned" into discrete distance classes, which are delimited by dist.breaks.

When gamma or omega are modeled using year-specific covariates, the covariate data for the final year will be ignored; however, they must be supplied.

If the time gap between primary periods is not constant, an M by T matrix of integers should be supplied using the primaryPeriod argument.

Value

an object of class unmarkedFrameDSO

See Also

unmarkedFrame-class, unmarkedFrame, distsampOpen

Examples

# Fake data
M <- 4 # number of sites
J <- 3 # number of distance classes
T <- 2 # number of primary periods

db <- c(0, 10, 20, 30) # distance break points

y <- matrix(c(
   5,4,3, 6,2,1, # In bin 1: 5 detections in primary period 1, 6 in period 2
   0,0,0, 0,1,0,
   2,1,1, 0,0,0,
   1,1,0, 1,1,1), nrow=M, ncol=J*T, byrow=TRUE)
y

# Primary periods of observations
# In this case there are no gaps
primPer <- matrix(as.integer(c(
    1,2,
    1,2,
    1,2,
    1,2)), nrow=M, ncol=T, byrow=TRUE)

#Site covs: M rows and 1 column per covariate
site.covs <- data.frame(x1=1:4, x2=factor(c('A','B','A','B')))
site.covs

#Yearly site covs on gamma/omega
ysc <- list(
    x3 = matrix(c(
        1,2,
        1,2,
        1,2,
        1,2), nrow=M, ncol=T, byrow=TRUE))

umf <- unmarkedFrameDSO(y=y, siteCovs=site.covs, yearlySiteCovs=ysc,
                        numPrimary=T, primaryPeriod=primPer,
                        dist.breaks=db, survey="point", unitsIn="m")            

umf                         # look at data
summary(umf)                # summarize

unmarked documentation built on July 9, 2023, 5:44 p.m.